Principles of Bioinformatics

COURSE OBJECTIVE
Are you interested in bioinformatics? Would you like know how huge amounts of data can be analysed in order to discover new biology? Would you like to solve open questions in scientific research? This course is open for any Bachelor student in a Science Degree (including Biology or Biochemistry).

Principles of Bioinformatics is the starting course for bioinformatics at an Academic level. It aims to give a broad overview of important topics relevant to the field, with a focus on current (open) problems in bioinformatics research. During the lectures and practical sessions you will become familiar with practical solutions, but also discover that there is still a lot of room for improvement in this rapidly advancing field of research.

Goals:

• To make the students aware of gaps in their own background knowledge.
• The student will be aware of the major issues, methodology and available algorithms in bioinformatics.
• To work together in a group of diverse backgrounds.
• To gain hands-on experience in scripting and handling basic mathematical equations as a means of solving bioinformatics problems.
• To develop a basic understanding of major concepts in genomics and molecular cell biology or to develop a basic scripting skills in python that are relevant to current topics in bioinformatics

COURSE CONTENT
Theory: Evolution, Genomes, Sequences, Biomolecular Structure, Biological Databases BLAST & PSI-BLAST, Protein domains & evolution, Next Generation Sequencing (NGS) or Massively Parallel Sequencing (MPS) and analysis

Practical: There are practicals sessions that aim to show you both existing solutions as well as open problems within the field of Bioinformatics. In the practicals you use existing databases and (web-server) solutions to solve biological problems. You will also use python scripts to automate queries to databases and web servers to investigate the value of current Bioinformatics Algorithms. We aim to organise the group project(s) in teams containing students with different BSc backgrounds.

The following topics are covered:

• Gene Ontology Database (GO) (python scripts)
• Homology Searching (web-based)
• BLAST / PSI-BLAST (python scripts)
• Benchmarking (python scripts)
• NGS (web-based)
• Network analysis

TEACHING METHODS
Lectures, project practicals, conversion classes in biology or python scripting

TYPE OF ASSESSMENT
[50%] Project (group work)
[50%] Oral or written exam (depending on number of course students) to assess:exercises, topics covered by the project and lecture topics

RECOMMENDED BACKGROUND KNOWLEDGE
An interest in programming and biological problems.

REMARKS
This course is part of the Minor Bioinformatics and Systems Biology Depending on the number of students, a large part of this course may be given together with the MSc course "Fundamentals of Bioinformatics". The assessment is at third year BSc level. This course is open for any Bachelor student in a Science Degree (including Biology or Biochemistry).